Reading info.rhd file...

Reading Intan Technologies RHD2000 Data File, Version 1.5

n signal groups 7
Found 32 amplifier channels.
Found 3 auxiliary input channels.
Found 1 supply voltage channel.
Found 0 board ADC channels.
Found 4 board digital input channels.
Found 0 board digital output channels.
Found 0 temperature sensors channels.

Header file contains no data.  Amplifiers were sampled at 30.00 kS/s.
Done!  Elapsed time: 0.0 seconds

Recording Info
--------------

amplifier_sampling_rate    30000.0
dig_in_sampling_rate       30000.0
notch_filter               60
ports                      
    C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C
channels                   
    0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31
num_channels               32
dig_in                     
    0, 1, 2, 3
file_type                  one file per channel

clustering_params.json not found in recording directory. Pulling parameters from defaults
spike_array_params.json not found in recording directory. Pulling parameters from defaults
psth_params.json not found in recording directory. Pulling parameters from defaults
pal_id_params.json not found in recording directory. Pulling parameters from defaults
CAR_params.json not found in recording directory. Pulling parameters from defaults
Writing parameters to JSON...Writing all parameters to json file in analysis_params folder...

Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p


Extract Intan Data
--------------------
Creating empty HDF5 store with raw data groups
Writing RN11_4taste_preCTA.h5 ...Done!

Creating empty arrays in hdf5 store for raw data...Done!
Extracting Intan data to HDF5 Store:
 h5 file: /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5

Reading time data...
Writing time data...Done!

----------
Extracting Digital Signal Data
----------
Reading digitalin data from board-DIN-00.dat...Done!
Writing data from ditigal in channel 0 to dig_in_0...Done!
Reading digitalin data from board-DIN-01.dat...Done!
Writing data from ditigal in channel 1 to dig_in_1...Done!
Reading digitalin data from board-DIN-02.dat...Done!
Writing data from ditigal in channel 2 to dig_in_2...Done!
Reading digitalin data from board-DIN-03.dat...Done!
Writing data from ditigal in channel 3 to dig_in_3...Done!
Done! Elapsed Time: 4.58


----------
Extracting Amplifier Signal Data
----------
Reading data from amp-C-000.dat...Done!
Writing data from port C channel 0 to electrode0...Done!
Reading data from amp-C-001.dat...Done!
Writing data from port C channel 1 to electrode1...Done!
Reading data from amp-C-002.dat...Done!
Writing data from port C channel 2 to electrode2...Done!
Reading data from amp-C-003.dat...Done!
Writing data from port C channel 3 to electrode3...Done!
Reading data from amp-C-004.dat...Done!
Writing data from port C channel 4 to electrode4...Done!
Reading data from amp-C-005.dat...Done!
Writing data from port C channel 5 to electrode5...Done!
Reading data from amp-C-006.dat...Done!
Writing data from port C channel 6 to electrode6...Done!
Reading data from amp-C-007.dat...Done!
Writing data from port C channel 7 to electrode7...Done!
Reading data from amp-C-008.dat...Done!
Writing data from port C channel 8 to electrode8...Done!
Reading data from amp-C-009.dat...Done!
Writing data from port C channel 9 to electrode9...Done!
Reading data from amp-C-010.dat...Done!
Writing data from port C channel 10 to electrode10...Done!
Reading data from amp-C-011.dat...Done!
Writing data from port C channel 11 to electrode11...Done!
Reading data from amp-C-012.dat...Done!
Writing data from port C channel 12 to electrode12...Done!
Reading data from amp-C-013.dat...Done!
Writing data from port C channel 13 to electrode13...Done!
Reading data from amp-C-014.dat...Done!
Writing data from port C channel 14 to electrode14...Done!
Reading data from amp-C-015.dat...Done!
Writing data from port C channel 15 to electrode15...Done!
Reading data from amp-C-016.dat...Done!
Writing data from port C channel 16 to electrode16...Done!
Reading data from amp-C-017.dat...Done!
Writing data from port C channel 17 to electrode17...Done!
Reading data from amp-C-018.dat...Done!
Writing data from port C channel 18 to electrode18...Done!
Reading data from amp-C-019.dat...Done!
Writing data from port C channel 19 to electrode19...Done!
Reading data from amp-C-020.dat...Done!
Writing data from port C channel 20 to electrode20...Done!
Reading data from amp-C-021.dat...Done!
Writing data from port C channel 21 to electrode21...Done!
Reading data from amp-C-022.dat...Done!
Writing data from port C channel 22 to electrode22...Done!
Reading data from amp-C-023.dat...Done!
Writing data from port C channel 23 to electrode23...Done!
Reading data from amp-C-024.dat...Done!
Writing data from port C channel 24 to electrode24...Done!
Reading data from amp-C-025.dat...Done!
Writing data from port C channel 25 to electrode25...Done!
Reading data from amp-C-026.dat...Done!
Writing data from port C channel 26 to electrode26...Done!
Reading data from amp-C-027.dat...Done!
Writing data from port C channel 27 to electrode27...Done!
Reading data from amp-C-028.dat...Done!
Writing data from port C channel 28 to electrode28...Done!
Reading data from amp-C-029.dat...Done!
Writing data from port C channel 29 to electrode29...Done!
Reading data from amp-C-030.dat...Done!
Writing data from port C channel 30 to electrode30...Done!
Reading data from amp-C-031.dat...Done!
Writing data from port C channel 31 to electrode31...Done!
Done! Elapsed Time: 54.38

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5...
Writing digital_input_map to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5...
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p


Data Extraction Complete
--------------------

----------
Gathering Trial Data and Creating Table
----------
Generating trial list for digital inputs: 0, 1, 2, 3
Constructing DataFrame...Done!
Writing data to h5 file...Done!
Done! Elapsed Time: 9.44

No digital output data found
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

Marking dead channels
----------
Marking eletrodes [] as dead.
They will be excluded from common average referencing.
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5...
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

CAR Groups

Group 0	Group 1
-------	-------
0	8
1	9
2	10
3	11
4	12
5	13
6	14
7	15
24	16
25	17
26	18
27	19
28	20
29	21
30	22
31	23

----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30, 31
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 56.26


----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 76.16


----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5 as /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5
Done! Elapsed Time: 113.61

Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p


Running Spike Detection
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      7
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Electrode    Result    Cutoff (s)
  0            1         2005
  1            1         2005
  2            1         2005
  3            1         2005
  4            1         2005
  5            1         2005
  6            1         2005
  7            1         2005
  8            1         2005
  9            1         2005
  10           1         2005
  11           1         2005
  12           1         2005
  13           1         2005
  14           1         2005
  15           1         2005
  16           1         2005
  17           1         2005
  18           1         2005
  19           1         2005
  20           1         2005
  21           1         2005
  22           1         2005
  23           1         2005
  24           1         2005
  25           1         2005
  26           1         2005
  27           1         2005
  28           1         2005
  29           1         2005
  30           1         2005
  31           1         2005
1 - Sucess
0 - No data or no spikes
-1 - Error
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5...
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

Spike Detection Complete
------------------

Running Blech Clust
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      11
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5...
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

Clustering Complete
------------------

----------
Clustering Cleanup
----------
Removing raw data from hdf5 store...Done!
Removing referenced data from hdf5 store...Done!

----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5 as /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA.h5
Done! Elapsed Time: 8.98

Done! Elapsed Time: 9.28

Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p


---------
Beginning unit similarity calculation
----------
Computing similarity between Unit 0 and Unit 0
Computing similarity between Unit 0 and Unit 1
Computing similarity between Unit 0 and Unit 2
Computing similarity between Unit 1 and Unit 0
Computing similarity between Unit 1 and Unit 1
Computing similarity between Unit 1 and Unit 2
Computing similarity between Unit 2 and Unit 0
Computing similarity between Unit 2 and Unit 1
Computing similarity between Unit 2 and Unit 2

Similarity calculation done!
No unit similarity violations found!
Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

Generating unit arrays with parameters:
----------
    dig_ins_to_use    
            0,     1,     2,     3
    laser_channels    
        
    sampling_rate     30000.0
    pre_stimulus      2000
    post_stimulus     5000
    

----------
Making Unit Spike Arrays
----------


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01

Creating spike arrays for dig_in_0...
Creating spike arrays for dig_in_1...
Creating spike arrays for dig_in_2...
Creating spike arrays for dig_in_3...
Done with spike array creation!
----------

Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

Saved RN11_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN11/RN11_4taste_preCTA_190520_141609/RN11_4taste_preCTA_dataset.p

